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GSOC Project Ideas 2020

Thu, 02/20/2020 - 18:41

← Older revision Revision as of 23:41, 20 February 2020 Line 153: Line 153:     == JBrowse 2 - Phylogenetic tree viewer == == JBrowse 2 - Phylogenetic tree viewer == −* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.+* ''Brief explanation:'' Comparative genomic data is arriving faster than ever, and building phylogenetic views directly into the user interface will be critical for evolutionary biologists to understand and interpret this data. This project will involve writing a new view for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree. * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Line 160: Line 160:  * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)    −== JBrowse 2 - Genomic Variant Effect Visualization ==+== JBrowse 2 - Ensembl VEP integration == −* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.+* ''Brief explanation:'' Predicting the impact - deleterious or neutral - of a genomic variant is an important task for clinical genomics. This project will add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. It will use integration with the Ensembl Variant Effect Predictor (VEP) via REST API to query and show predicted variant effects.  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Line 169: Line 169:     == JBrowse 2 - Genomic Variant Evidence Visualization == == JBrowse 2 - Genomic Variant Evidence Visualization == −* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Brief explanation:'' Drilling into the evidence for an individual variant will be a routine task in personalized genomic medicine. This project will add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.    * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Colin Diesh
Categories: Bio

2011 GMOD Spring Training

Tue, 02/11/2020 - 18:28

‎Schedule: type fix

← Older revision Revision as of 23:28, 11 February 2020 Line 67: Line 67:  <div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail: <div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail:    −'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull [[SOBA]]'''+'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull; [[SOBA]]'''  </div> </div>  |} |} Clements
Categories: Bio

Calendar

Tue, 02/11/2020 - 18:09

‎Other Calendars: Updated Galaxy events page link

← Older revision Revision as of 23:09, 11 February 2020 (One intermediate revision by the same user not shown)Line 20: Line 20:  * [https://www.google.com/calendar/feeds/mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com/public/basic Galaxy Calendar] [[File:RSSIcon16x16.gif|Galaxy Calendar Feed]] * [https://www.google.com/calendar/feeds/mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com/public/basic Galaxy Calendar] [[File:RSSIcon16x16.gif|Galaxy Calendar Feed]]    −  −==iAnn (Bioinformatics Events) Calendar==  −  −[http://iann.pro iAnn] lists events relevant to the broader scientific community.  −  −<iannwidget />        Line 32: Line 26:  {| {|  | | −* [http://wiki.galaxyproject.org/Events Galaxy events list]+* [http://galaxyproject.org/events Galaxy events list]  * [http://bioinformatics.oupjournals.org/cgi/calendarcontent Bioinformatics (journal) calender] * [http://bioinformatics.oupjournals.org/cgi/calendarcontent Bioinformatics (journal) calender]  * [http://www.embnet.org/event/all/list EMBnet events list] * [http://www.embnet.org/event/all/list EMBnet events list] Line 47: Line 41:  {{GMODEventsList}} {{GMODEventsList}}    −[[Category:GMOD Project]]+[[Category:GMOD_Project]] −[[Category:GMOD Community]]+[[Category:GMOD_Community]]  [[Category:Events]] [[Category:Events]] Clements
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 15:06

← Older revision Revision as of 20:06, 6 February 2020 (2 intermediate revisions by the same user not shown)Line 151: Line 151:  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== JBrowse 2 - Phylogenetic tree viewer ==  +* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  +* ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genomic Variant Effect Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Medium  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genomic Variant Evidence Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) RobertBuels
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 15:04

← Older revision Revision as of 20:04, 6 February 2020 (One intermediate revision by the same user not shown)Line 151: Line 151:  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== JBrowse 2 - Phylogenetic tree viewer ==  +* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  +* ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genome Variant Effect Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Medium  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genome Variant Evidence Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) RobertBuels
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 12:10

‎Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome)

← Older revision Revision as of 17:10, 6 February 2020 (10 intermediate revisions by the same user not shown)Line 52: Line 52:  **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).    −== Create a software package for use in R to query Reactome’s Graph Database in Neo4J ==+== Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome) ==     *'''Project Idea Name (Project Name/Lab Name)''' *'''Project Idea Name (Project Name/Lab Name)''' Line 60: Line 60:  **''Knowledge prerequisites:''  R Programming Language, Neo4J. **''Knowledge prerequisites:''  R Programming Language, Neo4J.  **''Skill level:'' Medium. **''Skill level:'' Medium. −**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).+**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca) and Guilherme Viteri (gviteri[AT]ebi.ac.uk).    − +== Automating Reactome’s data release post-step QA (Reactome) == −== Automating Reactome’s data release post-step QA ==+  * ''Brief explanation:'' * ''Brief explanation:''  ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. Line 74: Line 73:  * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)    −== GraphDB API for Reactome ==+== GraphDB API (Reactome) ==  * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.   * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.    * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. Line 81: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).  +   +== GraphQL interface for querying Reactome data (Reactome) ==  +* ''Brief explanation:'' Reactome currently has a REST-based API that allows end-users to obtain specific data from pre-defined queries.  To allow users to customize their queries, explore the Reactome data schema and better understand what data they can obtain, a GraphQL based endpoint could be added to the existing API.  +* ''Expected results:'' A publicly accessible GraphQL API that allows Reactome end-users to submit custom data queries to Reactome  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites: Java, GraphQL, Neo4j (preferred), Swagger (optional)''  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)  +   +== Statistics consolidation/display of release data (Reactome) ==  +* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology  +* ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Jweiser
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 10:48

‎Statistics consolidation and display of public release data (Reactome)

← Older revision Revision as of 15:48, 6 February 2020 (9 intermediate revisions by the same user not shown)Line 52: Line 52:  **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).    −== Create a software package for use in R to query Reactome’s Graph Database in Neo4J ==+== Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome) ==     *'''Project Idea Name (Project Name/Lab Name)''' *'''Project Idea Name (Project Name/Lab Name)''' Line 62: Line 62:  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).    − +== Automating Reactome’s data release post-step QA (Reactome) == −== Automating Reactome’s data release post-step QA ==+  * ''Brief explanation:'' * ''Brief explanation:''  ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. Line 74: Line 73:  * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)    −== GraphDB API for Reactome ==+== GraphDB API (Reactome) ==  * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.   * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.    * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. Line 81: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).  +   +== GraphQL interface for querying Reactome data (Reactome) ==  +* ''Brief explanation:'' Reactome currently has a REST-based API that allows end-users to obtain specific data from pre-defined queries.  To allow users to customize their queries, explore the Reactome data schema and better understand what data they can obtain, a GraphQL based endpoint could be added to the existing API.  +* ''Expected results:'' A publicly accessible GraphQL API that allows Reactome end-users to submit custom data queries to Reactome  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites: Java, GraphQL, Neo4j (preferred), Swagger (optional)''  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)  +   +== Statistics consolidation/display of release data (Reactome) ==  +* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology  +* ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Jweiser
Categories: Bio

GSOC Project Ideas 2020

Wed, 02/05/2020 - 15:41

‎GraphDB API for Reactome

← Older revision Revision as of 20:41, 5 February 2020 (2 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +  +== Automating Reactome’s data release post-step QA ==  +* ''Brief explanation:''  +** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly.  +** The project will involve the developer building QA steps that can automatically verify the data release steps ran correctly. The data release can be divided into MySQL or Neo4j components, and the student can choose to work on QA for either or both.  +* ''Expected results:'' QA code that automatically verifies release steps were correctly run. The new QA tests will encompass data checks within the MySQL and/or Neo4j databases as well as comparisons between data releases.  +* ''Project Home Page URL:'' https://reactome.org/  +* ''Project paper reference and URL:''  +* ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  +* ''Skill level:'' Medium  +* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)  +  +== GraphDB API for Reactome ==  +* ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.  +* ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API.  +* ''Project Home Page URL:'' [https://reactome.org/ reactome.org].  +* ''Project paper reference and URL:''  +* ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),     == Community data submission (WormBase) == == Community data submission (WormBase) == Sshorser
Categories: Bio

News/Prospecting for Proposals for GSoC 2015

Wed, 02/05/2020 - 12:01

← Older revision Revision as of 17:01, 5 February 2020 Line 7: Line 7:     If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! −  −{{NewsItem|2015/02/10}}  Scott
Categories: Bio

News/Prospecting for Proposals for GSoC 2016

Wed, 02/05/2020 - 11:38

← Older revision Revision as of 16:38, 5 February 2020 Line 8: Line 8:     If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! −  −{{NewsItem|2016/01/30}}  Scott
Categories: Bio

News/Prospecting for Proposals for GSoC 2017

Wed, 02/05/2020 - 11:38

← Older revision Revision as of 16:38, 5 February 2020 Line 8: Line 8:     If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! −  −{{NewsItem|2017/01/30}}  Scott
Categories: Bio

News/Prospecting for Proposals for GSoC 2020

Tue, 02/04/2020 - 01:42

← Older revision Revision as of 06:42, 4 February 2020 Line 8: Line 8:     If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice! If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice!  +  +{{NewsItem|2020/02/03}}     [[Category:GSOC]] [[Category:GSOC]]  [[Category:GSoC]] [[Category:GSoC]]  [[Category:News_Items]] [[Category:News_Items]] Robin.haw
Categories: Bio

News/Prospecting for Proposals for GSoC 2020

Tue, 02/04/2020 - 01:41

Created page with "link=GSoC The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Goo..."

New page

[[File:GoogleSummer_2016logo.jpg|272px|right|link=GSoC]]

The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Google Summer of Code (GSoC)] this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the [[GSoC|GSoC wiki page]] and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] [mailto:help@gmod.org help@gmod.org].

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice!

[[Category:GSOC]]
[[Category:GSoC]]
[[Category:News_Items]] Robin.haw
Categories: Bio

GSOC Project Ideas 2020

Mon, 02/03/2020 - 17:25

‎GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources)

← Older revision Revision as of 22:25, 3 February 2020 (12 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +== Community data submission (WormBase) ==  +* ''Brief explanation:'' WormBase is a comprehensive research knowledgebase on the biology of nematodes. Our database is built by extracting and standardizing information from published literature, which is time consuming and low throughput. Hence, we would like to encourage our users, who also derive the knowledge originally, to submit their findings through our website. This would speed up the integration of knowledge in our database and diversify our data sources.  +* ''Expected results:'' Website frontend components and backend mechanisms that allow inline data submission from users, realtime update of the website, notification and mechanism for review and integrate the data into WormBase database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Data Table functionality and performance (WormBase) ==  +* ''Brief explanation'': WormBase is a comprehensive research knowledgebase on the biology of nematodes. Biologists access our vast information through a web port which often provides information in many tables. Here is an example page of a well-studied gene in C. elegans, dat-6, https://wormbase.org/species/c_elegans/gene/WBGene00000912#01347b--10. These tables where developed years ago based on HTML and jQuery, with certain features depending on Flash. Their limitations and usability issues are more pronounced now. Hence, we are looking for a new implementation of these tables with React, which is used in many parts of the site.  +* ''Expected results:'' A generic and customizable table component in React for displaying WormBase data, with the ability to search, filter, sort, paginate, and export all or parts of the table.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, CSS, React.  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources) ==  +* ''Brief explanation:'' As a data resource, we seek to make our data accessible through web APIs. [https://graphql.org/ GraphQL], a new web API specification, provides programmatic access users a powerful way to retrieve our data. However, a single monolithic GraphQL service will be difficult for us to manage due to heterogeneous data types and geographically distributed teams. We would like to allow different teams (each organized around a knowledge domain) to independently develop and deploy GraphQL services, and combine them into a single GraphQL schema and API endpoint that can be queried easily cross-domain. [https://www.apollographql.com/docs/apollo-server/federation/introduction/ Apollo Federation] seems to be what we need, and we’d like to assess its viability as a solution to our problem.  +* ''Expected results:'' Prototype for expressing multiple independently developed and deployed GraphQL services as a single graph using Apollo Federation.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, microservice architecture.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Single Sign On (WormBase) ==  +* ''Brief explanation:'' WormBase consists of an ecosystem of tools, some of which we developed ourselves, others we adopted from the community. Several of these tools require a user to be signed in, giving rise to multiple implementations of authentication and unnecessary difficulties in user experience.  +* ''Expected results:'' That users only need to sign-in once on WormBase. We would like to have a centrally managed authentication service that allows individual services to manage their own authorization. And we would need a migration plan for the tools that currently manages its own authentication.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' Authentication and Authorization (JWT, OAuth2).  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Faster Autocompletion (WormBase Name Service) ==  +* ''Brief explanation:'' As a biological knowledge base, WormBase uses unique stable identifiers to biological entities described in scientific publications (such a s gene or a variation, etc). The tasks to create an identifier and to lookup information associated with it (such as its common name and metadata) is handled by a tool, called the Name Service. The performance of the Name Service is currently hindered by the slowness of the autocompletion, which is performed directly on the database that is not optimized for this type of query. We are looking to implement an autocomplete solution using a search engine, such as Elasticsearch.  +* ''Expected results:'' A faster REST API to retrieve autocomplete suggestions from, and the necessary workflow to ensure the search engine highly available and up-to-date with the database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' Elasticsearch, Clojure (or another LISP)  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Word and sentence completion for curatorial remarks (WormBase Name Service) ==  +* ''Brief explanation:'' As a biological research knowledgebase, WormBase aggregates and standardizes experimental findings reported in research literature. This work is often done with the help of our curators, who, in addition to filling in standardized forms, write free-text remarks providing additional context. We would like a word and sentence completion tool that reduces the amount of repetitive typing that a curator does, without hindering their ability to compose original content if they so choose.  +* ''Expected results:'' An performant in-browser word and sentence completion tool, similar to [https://research.google/pubs/pub48231/ Gmail Smart Compose], that suggest words based on previously composed content, available through an API.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' NLP, JavaScript  +* ''Skill level:'' Advanced  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). Sibyl
Categories: Bio

GSOC Project Ideas 2020

Mon, 02/03/2020 - 17:05

‎Data Table functionality and performance (WormBase)

← Older revision Revision as of 22:05, 3 February 2020 (4 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +== Community data submission (WormBase) ==  +* ''Brief explanation:'' WormBase is a comprehensive research knowledgebase on the biology of nematodes. Our database is built by extracting and standardizing information from published literature, which is time consuming and low throughput. Hence, we would like to encourage our users, who also derive the knowledge originally, to submit their findings through our website. This would speed up the integration of knowledge in our database and diversify our data sources.  +* ''Expected results:'' Website frontend components and backend mechanisms that allow inline data submission from users, realtime update of the website, notification and mechanism for review and integrate the data into WormBase database.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred.  +* ''Skill level:'' Advanced  +* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org).  +  +== Data Table functionality and performance (WormBase) ==  +* ''Brief explanation'': WormBase is a comprehensive research knowledgebase on the biology of nematodes. Biologists access our vast information through a web port which often provides information in many tables. Here is an example page of a well-studied gene in C. elegans, dat-6, https://wormbase.org/species/c_elegans/gene/WBGene00000912#01347b--10. These tables where developed years ago based on HTML and jQuery, with certain features depending on Flash. Their limitations and usability issues are more pronounced now. Hence, we are looking for a new implementation of these tables with React, which is used in many parts of the site.  +* ''Expected results:'' A generic and customizable table component in React for displaying WormBase data, with the ability to search, filter, sort, paginate, and export all or parts of the table.  +* ''Project Home Page URL:'' https://wormbase.org  +* ''Project paper reference and URL:'' https://academic.oup.com/nar/article/48/D1/D762/5603222  +* ''Knowledge prerequisites:'' JavaScript, CSS, React.  +* ''Skill level:'' Medium  +* ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== GraphQL over Microservice Architecture (WormBase / Alliance of Genome Resources) ==  +  +== Single Sign On (WormBase) ==  +  +== Faster Autocompletion (WormBase Name Service) ==  +  +== Word and sentence completion for curatorial remarks (WormBase Name Service) == Sibyl
Categories: Bio

User:Miharimamy

Mon, 02/03/2020 - 16:28

Creating user page for new user.

New page

Microbiologist and fullstack developer, my field of research evolves around knowledge representation and data mining applied to bioinformatics and health informatics.
I got a master degree in biotechnology and a bachelor degree in computer science mainly because the bioinformatic major was not open yet at the time. So I decided to mix in my love of biology with my programming skills through a PhD in Genomics and Bioinformatics.
To brush up my skills, I got a year-long experience in a tech company as a fullstack developer in JavaScript and get the good practices for application industry standards.
I like sharing and collaborating with passionate people like myself about various subjects : art, math, physics, biology and obviously computer science. Scott
Categories: Bio

User:Miharimamy

Mon, 02/03/2020 - 16:28

User account Miharimamy was created by Scott

Scott
Categories: Bio

User:Sibyl

Mon, 02/03/2020 - 16:13

Creating user page for new user.

New page

Software Developer @ WormBase. I completed my undergraduate in Microbiology and Computer Science at University of British Columbia. My expertise is in full-stack web development, cloud computing (AWS) and exploratory/visual data analysis. I am a user experience enthusiast, always seeking ways to make our product better by trying to understand our users more. Scott
Categories: Bio

User:Sibyl

Mon, 02/03/2020 - 16:13

User account Sibyl was created by Scott

Scott
Categories: Bio

GSOC Project Ideas 2020

Wed, 01/29/2020 - 11:21

← Older revision Revision as of 16:21, 29 January 2020 Line 60: Line 60:  **''Knowledge prerequisites:''  R Programming Language, Neo4J. **''Knowledge prerequisites:''  R Programming Language, Neo4J.  **''Skill level:'' Medium. **''Skill level:'' Medium. −**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca) and Antonio Fabregat (fabregat[AT]ebi.ac.uk).+**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). Jweiser
Categories: Bio

Pages